Crash course for using the ILRI, Kenya research computing cluster. Target audience was new biologists who have Illumina MiSeq data to analyze on the cluster, but were completely new to Linux (and come from a Windows/non-technical background).
– make directory mv – move a file or directory cp – copy a file or folder rm - remove a file whoami – print the name of the current user who – print a list of other users who are logged in date – print the current date and time on the server echo – print text to the screen
to change the behavior of the command. Arguments are separated by one or more spaces: mkdir data Some commands require arguments (they don’t make sense to run by themselves, like mkdir).
ls)! - Attention to detail (ls -l vs ls --l)! - Pasting from Word (“pretty” quotes, etc)! - Missing spaces - Using Windows-isms (\ vs /)! Google is your friend!
Simple Linux Utility for Resource Management - Manages CPUs and jobs on the cluster - Ensures everyone plays fair - Everyone gets ~20 CPUs by default - More info: http://hpc.ilri.cgiar.org/using-slurm Some commands: interactive - allocates resources for interactive shell (1 CPU) squeue - see a list of running / queued jobs scancel - cancel a job sbatch - submit a “batch” job (ie, not interactive)
friend) - Try not to write to your home folder - Don’t run jobs on the head node (HPC) - If you crash the cluster you buy cookies for Alan - Don’t talk about HPC Club